{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Incidence du syndrome grippal" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [], "source": [ "%matplotlib inline\n", "import matplotlib.pyplot as plt\n", "import pandas as pd\n", "import isoweek" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Les données de l'incidence du syndrome grippal sont disponibles du site Web du [Réseau Sentinelles](http://www.sentiweb.fr/). Nous les récupérons sous forme d'un fichier en format CSV dont chaque ligne correspond à une semaine de la période demandée. Nous téléchargeons toujours le jeu de données complet, qui commence en 1984 et se termine avec une semaine récente." ] }, { "cell_type": "code", "execution_count": 16, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Données déjà présentes sur le disque, chargement...\n" ] } ], "source": [ "data_url = \"http://www.sentiweb.fr/datasets/incidence-PAY-3.csv\"\n", "\n", "data_path = \"./incidence-PAY-3.csv\"\n", "\n", "try:\n", " data = pd.read_csv(data_path)\n", " print(\"Données déjà présentes sur le disque, chargement...\")\n", "except FileNotFoundError as e:\n", " print(\"Données non présentes, téléchargement...\")\n", " data = pd.read_csv(data_url)\n", " data.to_csv(data_path)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Voici l'explication des colonnes données [sur le site d'origine](https://ns.sentiweb.fr/incidence/csv-schema-v1.json):\n", "\n", "| Nom de colonne | Libellé de colonne |\n", "|----------------|-----------------------------------------------------------------------------------------------------------------------------------|\n", "| week | Semaine calendaire (ISO 8601) |\n", "| indicator | Code de l'indicateur de surveillance |\n", "| inc | Estimation de l'incidence de consultations en nombre de cas |\n", "| inc_low | Estimation de la borne inférieure de l'IC95% du nombre de cas de consultation |\n", "| inc_up | Estimation de la borne supérieure de l'IC95% du nombre de cas de consultation |\n", "| inc100 | Estimation du taux d'incidence du nombre de cas de consultation (en cas pour 100,000 habitants) |\n", "| inc100_low | Estimation de la borne inférieure de l'IC95% du taux d'incidence du nombre de cas de consultation (en cas pour 100,000 habitants) |\n", "| inc100_up | Estimation de la borne supérieure de l'IC95% du taux d'incidence du nombre de cas de consultation (en cas pour 100,000 habitants) |\n", "| geo_insee | Code de la zone géographique concernée (Code INSEE) http://www.insee.fr/fr/methodes/nomenclatures/cog/ |\n", "| geo_name | Libellé de la zone géographique (ce libellé peut être modifié sans préavis) |\n", "\n", "La première ligne du fichier CSV est un commentaire, que nous ignorons en précisant `skiprows=1`." ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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weekindicatorincinc_lowinc_upinc100inc100_lowinc100_upgeo_inseegeo_name
020244138468374972.094394.0127112.0142.0FRFrance
120244038489576454.093336.0127114.0140.0FRFrance
220243939166082937.0100383.0137124.0150.0FRFrance
320243839178682903.0100669.0138125.0151.0FRFrance
420243735646049319.063601.08574.096.0FRFrance
520243633365727906.039408.05041.059.0FRFrance
620243532740422036.032772.04133.049.0FRFrance
720243432671721003.032431.04031.049.0FRFrance
820243332062315349.025897.03123.039.0FRFrance
920243232318717532.028842.03527.043.0FRFrance
1020243132603520267.031803.03930.048.0FRFrance
1120243033639328593.044193.05543.067.0FRFrance
1220242933956032592.046528.05949.069.0FRFrance
1320242835434245781.062903.08168.094.0FRFrance
1420242734736440234.054494.07160.082.0FRFrance
1520242634421936956.051482.06655.077.0FRFrance
1620242534720440300.054108.07161.081.0FRFrance
1720242434111034671.047549.06252.072.0FRFrance
1820242333587530610.041140.05446.062.0FRFrance
1920242233377228274.039270.05143.059.0FRFrance
2020242132196317556.026370.03326.040.0FRFrance
2120242032005715780.024334.03024.036.0FRFrance
2220241931537511274.019476.02317.029.0FRFrance
2320241832240917653.027165.03427.041.0FRFrance
2420241732704221410.032674.04133.049.0FRFrance
2520241632888223305.034459.04335.051.0FRFrance
2620241533022924648.035810.04537.053.0FRFrance
2720241433181326529.037097.04840.056.0FRFrance
2820241333509029607.040573.05345.061.0FRFrance
2920241234063934582.046696.06152.070.0FRFrance
.................................
205519852132609619621.032571.04735.059.0FRFrance
205619852032789620885.034907.05138.064.0FRFrance
205719851934315432821.053487.07859.097.0FRFrance
205819851834055529935.051175.07455.093.0FRFrance
205919851733405324366.043740.06244.080.0FRFrance
206019851635036236451.064273.09166.0116.0FRFrance
206119851536388145538.082224.011683.0149.0FRFrance
20621985143134545114400.0154690.0244207.0281.0FRFrance
20631985133197206176080.0218332.0357319.0395.0FRFrance
20641985123245240223304.0267176.0445405.0485.0FRFrance
20651985113276205252399.0300011.0501458.0544.0FRFrance
20661985103353231326279.0380183.0640591.0689.0FRFrance
20671985093369895341109.0398681.0670618.0722.0FRFrance
20681985083389886359529.0420243.0707652.0762.0FRFrance
20691985073471852432599.0511105.0855784.0926.0FRFrance
20701985063565825518011.0613639.01026939.01113.0FRFrance
20711985053637302592795.0681809.011551074.01236.0FRFrance
20721985043424937390794.0459080.0770708.0832.0FRFrance
20731985033213901174689.0253113.0388317.0459.0FRFrance
207419850239758680949.0114223.0177147.0207.0FRFrance
207519850138548965918.0105060.0155120.0190.0FRFrance
207619845238483060602.0109058.0154110.0198.0FRFrance
2077198451310172680242.0123210.0185146.0224.0FRFrance
20781984503123680101401.0145959.0225184.0266.0FRFrance
2079198449310107381684.0120462.0184149.0219.0FRFrance
208019844837862060634.096606.0143110.0176.0FRFrance
208119844737202954274.089784.013199.0163.0FRFrance
208219844638733067686.0106974.0159123.0195.0FRFrance
20831984453135223101414.0169032.0246184.0308.0FRFrance
208419844436842220056.0116788.012537.0213.0FRFrance
\n", "

2085 rows × 10 columns

\n", "
" ], "text/plain": [ " week indicator inc inc_low inc_up inc100 inc100_low \\\n", "0 202441 3 84683 74972.0 94394.0 127 112.0 \n", "1 202440 3 84895 76454.0 93336.0 127 114.0 \n", "2 202439 3 91660 82937.0 100383.0 137 124.0 \n", "3 202438 3 91786 82903.0 100669.0 138 125.0 \n", "4 202437 3 56460 49319.0 63601.0 85 74.0 \n", "5 202436 3 33657 27906.0 39408.0 50 41.0 \n", "6 202435 3 27404 22036.0 32772.0 41 33.0 \n", "7 202434 3 26717 21003.0 32431.0 40 31.0 \n", "8 202433 3 20623 15349.0 25897.0 31 23.0 \n", "9 202432 3 23187 17532.0 28842.0 35 27.0 \n", "10 202431 3 26035 20267.0 31803.0 39 30.0 \n", "11 202430 3 36393 28593.0 44193.0 55 43.0 \n", "12 202429 3 39560 32592.0 46528.0 59 49.0 \n", "13 202428 3 54342 45781.0 62903.0 81 68.0 \n", "14 202427 3 47364 40234.0 54494.0 71 60.0 \n", "15 202426 3 44219 36956.0 51482.0 66 55.0 \n", "16 202425 3 47204 40300.0 54108.0 71 61.0 \n", "17 202424 3 41110 34671.0 47549.0 62 52.0 \n", "18 202423 3 35875 30610.0 41140.0 54 46.0 \n", "19 202422 3 33772 28274.0 39270.0 51 43.0 \n", "20 202421 3 21963 17556.0 26370.0 33 26.0 \n", "21 202420 3 20057 15780.0 24334.0 30 24.0 \n", "22 202419 3 15375 11274.0 19476.0 23 17.0 \n", "23 202418 3 22409 17653.0 27165.0 34 27.0 \n", "24 202417 3 27042 21410.0 32674.0 41 33.0 \n", "25 202416 3 28882 23305.0 34459.0 43 35.0 \n", "26 202415 3 30229 24648.0 35810.0 45 37.0 \n", "27 202414 3 31813 26529.0 37097.0 48 40.0 \n", "28 202413 3 35090 29607.0 40573.0 53 45.0 \n", "29 202412 3 40639 34582.0 46696.0 61 52.0 \n", "... ... ... ... ... ... ... ... \n", "2055 198521 3 26096 19621.0 32571.0 47 35.0 \n", "2056 198520 3 27896 20885.0 34907.0 51 38.0 \n", "2057 198519 3 43154 32821.0 53487.0 78 59.0 \n", "2058 198518 3 40555 29935.0 51175.0 74 55.0 \n", "2059 198517 3 34053 24366.0 43740.0 62 44.0 \n", "2060 198516 3 50362 36451.0 64273.0 91 66.0 \n", "2061 198515 3 63881 45538.0 82224.0 116 83.0 \n", "2062 198514 3 134545 114400.0 154690.0 244 207.0 \n", "2063 198513 3 197206 176080.0 218332.0 357 319.0 \n", "2064 198512 3 245240 223304.0 267176.0 445 405.0 \n", "2065 198511 3 276205 252399.0 300011.0 501 458.0 \n", "2066 198510 3 353231 326279.0 380183.0 640 591.0 \n", "2067 198509 3 369895 341109.0 398681.0 670 618.0 \n", "2068 198508 3 389886 359529.0 420243.0 707 652.0 \n", "2069 198507 3 471852 432599.0 511105.0 855 784.0 \n", "2070 198506 3 565825 518011.0 613639.0 1026 939.0 \n", "2071 198505 3 637302 592795.0 681809.0 1155 1074.0 \n", "2072 198504 3 424937 390794.0 459080.0 770 708.0 \n", "2073 198503 3 213901 174689.0 253113.0 388 317.0 \n", "2074 198502 3 97586 80949.0 114223.0 177 147.0 \n", "2075 198501 3 85489 65918.0 105060.0 155 120.0 \n", "2076 198452 3 84830 60602.0 109058.0 154 110.0 \n", "2077 198451 3 101726 80242.0 123210.0 185 146.0 \n", "2078 198450 3 123680 101401.0 145959.0 225 184.0 \n", "2079 198449 3 101073 81684.0 120462.0 184 149.0 \n", "2080 198448 3 78620 60634.0 96606.0 143 110.0 \n", "2081 198447 3 72029 54274.0 89784.0 131 99.0 \n", "2082 198446 3 87330 67686.0 106974.0 159 123.0 \n", "2083 198445 3 135223 101414.0 169032.0 246 184.0 \n", "2084 198444 3 68422 20056.0 116788.0 125 37.0 \n", "\n", " inc100_up geo_insee geo_name \n", "0 142.0 FR France \n", "1 140.0 FR France \n", "2 150.0 FR France \n", "3 151.0 FR France \n", "4 96.0 FR France \n", "5 59.0 FR France \n", "6 49.0 FR France \n", "7 49.0 FR France \n", "8 39.0 FR France \n", "9 43.0 FR France \n", "10 48.0 FR France \n", "11 67.0 FR France \n", "12 69.0 FR France \n", "13 94.0 FR France \n", "14 82.0 FR France \n", "15 77.0 FR France \n", "16 81.0 FR France \n", "17 72.0 FR France \n", "18 62.0 FR France \n", "19 59.0 FR France \n", "20 40.0 FR France \n", "21 36.0 FR France \n", "22 29.0 FR France \n", "23 41.0 FR France \n", "24 49.0 FR France \n", "25 51.0 FR France \n", "26 53.0 FR France \n", "27 56.0 FR France \n", "28 61.0 FR France \n", "29 70.0 FR France \n", "... ... ... ... \n", "2055 59.0 FR France \n", "2056 64.0 FR France \n", "2057 97.0 FR France \n", "2058 93.0 FR France \n", "2059 80.0 FR France \n", "2060 116.0 FR France \n", "2061 149.0 FR France \n", "2062 281.0 FR France \n", "2063 395.0 FR France \n", "2064 485.0 FR France \n", "2065 544.0 FR France \n", "2066 689.0 FR France \n", "2067 722.0 FR France \n", "2068 762.0 FR France \n", "2069 926.0 FR France \n", "2070 1113.0 FR France \n", "2071 1236.0 FR France \n", "2072 832.0 FR France \n", "2073 459.0 FR France \n", "2074 207.0 FR France \n", "2075 190.0 FR France \n", "2076 198.0 FR France \n", "2077 224.0 FR France \n", "2078 266.0 FR France \n", "2079 219.0 FR France \n", "2080 176.0 FR France \n", "2081 163.0 FR France \n", "2082 195.0 FR France \n", "2083 308.0 FR France \n", "2084 213.0 FR France \n", "\n", "[2085 rows x 10 columns]" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "raw_data = pd.read_csv(data_url, skiprows=1)\n", "raw_data" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Y a-t-il des points manquants dans ce jeux de données ? Oui, la semaine 19 de l'année 1989 n'a pas de valeurs associées." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "raw_data[raw_data.isnull().any(axis=1)]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Nous éliminons ce point, ce qui n'a pas d'impact fort sur notre analyse qui est assez simple." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "data = raw_data.dropna().copy()\n", "data" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Nos données utilisent une convention inhabituelle: le numéro de\n", "semaine est collé à l'année, donnant l'impression qu'il s'agit\n", "de nombre entier. C'est comme ça que Pandas les interprète.\n", " \n", "Un deuxième problème est que Pandas ne comprend pas les numéros de\n", "semaine. Il faut lui fournir les dates de début et de fin de\n", "semaine. Nous utilisons pour cela la bibliothèque `isoweek`.\n", "\n", "Comme la conversion des semaines est devenu assez complexe, nous\n", "écrivons une petite fonction Python pour cela. Ensuite, nous\n", "l'appliquons à tous les points de nos donnés. Les résultats vont\n", "dans une nouvelle colonne 'period'." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "def convert_week(year_and_week_int):\n", " year_and_week_str = str(year_and_week_int)\n", " year = int(year_and_week_str[:4])\n", " week = int(year_and_week_str[4:])\n", " w = isoweek.Week(year, week)\n", " return pd.Period(w.day(0), 'W')\n", "\n", "data['period'] = [convert_week(yw) for yw in data['week']]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Il restent deux petites modifications à faire.\n", "\n", "Premièrement, nous définissons les périodes d'observation\n", "comme nouvel index de notre jeux de données. Ceci en fait\n", "une suite chronologique, ce qui sera pratique par la suite.\n", "\n", "Deuxièmement, nous trions les points par période, dans\n", "le sens chronologique." ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [ "sorted_data = data.set_index('period').sort_index()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Nous vérifions la cohérence des données. Entre la fin d'une période et\n", "le début de la période qui suit, la différence temporelle doit être\n", "zéro, ou au moins très faible. Nous laissons une \"marge d'erreur\"\n", "d'une seconde.\n", "\n", "Ceci s'avère tout à fait juste sauf pour deux périodes consécutives\n", "entre lesquelles il manque une semaine.\n", "\n", "Nous reconnaissons ces dates: c'est la semaine sans observations\n", "que nous avions supprimées !" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "periods = sorted_data.index\n", "for p1, p2 in zip(periods[:-1], periods[1:]):\n", " delta = p2.to_timestamp() - p1.end_time\n", " if delta > pd.Timedelta('1s'):\n", " print(p1, p2)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Un premier regard sur les données !" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "sorted_data['inc'].plot()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Un zoom sur les dernières années montre mieux la situation des pics en hiver. Le creux des incidences se trouve en été." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "sorted_data['inc'][-200:].plot()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Etude de l'incidence annuelle" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Etant donné que le pic de l'épidémie se situe en hiver, à cheval\n", "entre deux années civiles, nous définissons la période de référence\n", "entre deux minima de l'incidence, du 1er août de l'année $N$ au\n", "1er août de l'année $N+1$.\n", "\n", "Notre tâche est un peu compliquée par le fait que l'année ne comporte\n", "pas un nombre entier de semaines. Nous modifions donc un peu nos périodes\n", "de référence: à la place du 1er août de chaque année, nous utilisons le\n", "premier jour de la semaine qui contient le 1er août.\n", "\n", "Comme l'incidence de syndrome grippal est très faible en été, cette\n", "modification ne risque pas de fausser nos conclusions.\n", "\n", "Encore un petit détail: les données commencent an octobre 1984, ce qui\n", "rend la première année incomplète. Nous commençons donc l'analyse en 1985." ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [ "first_august_week = [pd.Period(pd.Timestamp(y, 8, 1), 'W')\n", " for y in range(1985,\n", " sorted_data.index[-1].year)]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "En partant de cette liste des semaines qui contiennent un 1er août, nous obtenons nos intervalles d'environ un an comme les périodes entre deux semaines adjacentes dans cette liste. Nous calculons les sommes des incidences hebdomadaires pour toutes ces périodes.\n", "\n", "Nous vérifions également que ces périodes contiennent entre 51 et 52 semaines, pour nous protéger contre des éventuelles erreurs dans notre code." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "year = []\n", "yearly_incidence = []\n", "for week1, week2 in zip(first_august_week[:-1],\n", " first_august_week[1:]):\n", " one_year = sorted_data['inc'][week1:week2-1]\n", " assert abs(len(one_year)-52) < 2\n", " yearly_incidence.append(one_year.sum())\n", " year.append(week2.year)\n", "yearly_incidence = pd.Series(data=yearly_incidence, index=year)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Voici les incidences annuelles." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "yearly_incidence.plot(style='*')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Une liste triée permet de plus facilement répérer les valeurs les plus élevées (à la fin)." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "yearly_incidence.sort_values()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Enfin, un histogramme montre bien que les épidémies fortes, qui touchent environ 10% de la population\n", " française, sont assez rares: il y en eu trois au cours des 35 dernières années." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "yearly_incidence.hist(xrot=20)" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.4" } }, "nbformat": 4, "nbformat_minor": 1 }